Cleland Introduction to R

About me

• Member of the Faculty, NYU Grossman School of Medicine, Department of Populatio Health, Division of Biostatistics
• Center for Drug Use and HIV Research, Director of the Transdisciplinary Methods Core
• Research and Methods Interests
  • HIV prevention and care
  • health disparities
  • meta-analysis
  • longitudinal data analysis
• Contact
  • email: Charles.Cleland@nyulangone.org
  • phone: 212-646-3692
  • location: 180 Madison Avenue, Room 2-53
• Curriculum Vitae

Goals for Today

• What is R
• R vs. R Studio
• Basics
• Getting data into and out of R
• Data management with R
• Making plots with R
• Common statistical analyses done in R (e.g., t-tests, regression)
• R packages
• Resources to learn more and the possibility of an ongoing R interest group

What is R?

• A statistical computing language and environment
• Windows, Mac, Unix, Linux
• Open source
• Organized into packages of functions and other objects

R vs. R Studio

• R is a statistical computing environment, with functions organized in packages to carry out a broad array of analytic work
• R Studio is a populatio integrated development environment (IDE) for R which adds workflow functionality and makes for a smoother user experience

Basics

Basic Operations

1 + 2 + 3

[1] 6

1 + 2 * 3

[1] 7

(1 + 2) * 3

[1] 9

c(0,1,2,3,5,8)

[1] 0 1 2 3 5 8

1:11

 [1]  1  2  3  4  5  6  7  8  9 10 11

1:11 + 3

 [1]  4  5  6  7  8  9 10 11 12 13 14

Assignment

x <- 3
y <- 1:10
z <- c(1,20,3,6)

Evaluation

x

[1] 3

y

 [1]  1  2  3  4  5  6  7  8  9 10

z

[1]  1 20  3  6

x + y

 [1]  4  5  6  7  8  9 10 11 12 13

x * z

[1]  3 60  9 18

Getting help within R

?mean
help(mean)

Types of R Objects

• Data frame
  • Like the typical two-dimensional table of data in other programs
• Vector
• matrix
  • Also a two dimensional table of data, but every variable is of the same type
• List
  • A way to combine objects, possibly of different types, into a composite object
  • Very powerful because you can apply functions to lists
  • Provides ways to get a great deal accomplished with very concise code
• Function

Types of R variables in Data Frames

• Character

my.character <- c('Emma','Olivia','Sophia')
my.character

[1] "Emma"   "Olivia" "Sophia"

• Date

my.dates <- c(as.Date("2012-04-05"), Sys.Date())
my.dates

[1] "2012-04-05" "2020-02-02"

• Numeric

my.numeric <- c(12,62.3,7,101)
my.numeric

[1]  12.0  62.3   7.0 101.0

• Factor

my.factor <- factor(c(0,0,0,1,1), labels=c('Female','Male'))
my.factor

[1] Female Female Female Male   Male  
Levels: Female Male

• Logical

my.logical <- c(TRUE,FALSE,FALSE)
my.logical

[1]  TRUE FALSE FALSE

Vectorized Arithmetic

weight.kg <- c(60, 72, 57, 90, 95, 72)
height.meters <- c(1.75, 1.80, 1.65, 1.90, 1.74, 1.91)
bmi <- weight.kg/height.meters^2
bmi

[1] 19.59184 22.22222 20.93664 24.93075 31.37799 19.73630

• Works element by element in the weight.kg and height.meters vectors
• There is no need for a loop

Make simple R objects

byear <- c(68,69,71,72)
byear

[1] 68 69 71 72

Boys <- data.frame(kid = c('JHC','CMC','REC','WBC'), 
                   byear = c(68,69,70,71))
Boys

  kid byear
1 JHC    68
2 CMC    69
3 REC    70
4 WBC    71

Access names and types of variables in a data frame

names(Boys)

[1] "kid"   "byear"

str(Boys)

'data.frame':   4 obs. of  2 variables:
 $ kid  : Factor w/ 4 levels "CMC","JHC","REC",..: 2 1 3 4
 $ byear: num  68 69 70 71

Accessing variables in data frames

Boys$kid

[1] JHC CMC REC WBC
Levels: CMC JHC REC WBC

with(Boys, mean(byear))

[1] 69.5

The R Workspace

• Objects you create are stored in a workspace
• R allows working with multiple objects at once, not just a single dataset
• Here is how to show what is in the workspace at any given point:

ls()

 [1] "bmi"           "Boys"          "byear"         "height.meters"
 [5] "my.character"  "my.dates"      "my.factor"     "my.logical"   
 [9] "my.numeric"    "weight.kg"     "x"             "y"            
[13] "z"            

• When you load packages, the objects in those packages are in different workspaces
• I am going to load a package called haven which has functions for reading data from and writing data to other formats

library(haven)

• I just made the objects in the haven package available
• I can see what those objects are (all functions) using a variation of the ls() command:

ls("package:haven")

 [1] "as_factor"        "format_tagged_na" "is.labelled"      "is_tagged_na"    
 [5] "labelled"         "labelled_spss"    "na_tag"           "print_labels"    
 [9] "print_tagged_na"  "read_dta"         "read_por"         "read_sas"        
[13] "read_sav"         "read_spss"        "read_stata"       "read_xpt"        
[17] "tagged_na"        "write_dta"        "write_sas"        "write_sav"       
[21] "write_xpt"        "zap_empty"        "zap_formats"      "zap_label"       
[25] "zap_labels"       "zap_missing"      "zap_widths"      

Getting data into R

• read.table for plain text (comma or tab delimited)
• read_sav for SPSS (haven package)
• read_dta for Stata (haven package)
• read.xlsx for MS-Excel (openxlsx package)
• Many other formats and connections to databases

read.table

mytable <- read.table("c:/chuck/NYU/Stat Group/table1.txt", sep=",", header=TRUE)
mytable

  id female inc80 inc81 inc82
1  1      0  5000  5500  6000
2  2      1  2000  2200  3300
3  3      0  3000  2000  1000

str(mytable)

'data.frame':   3 obs. of  5 variables:
 $ id    : int  1 2 3
 $ female: int  0 1 0
 $ inc80 : int  5000 2000 3000
 $ inc81 : int  5500 2200 2000
 $ inc82 : int  6000 3300 1000

read_sav

library(haven)
titanic <- read_sav("c:/chuck/NYU/Stat Group/titanic.sav")
head(titanic)

# A tibble: 6 x 5
     pclass  survived    age  fare     gender
  <dbl+lbl> <dbl+lbl>  <dbl> <dbl>  <dbl+lbl>
1 1 [First]   1 [Yes] 29     211.  1 [Female]
2 1 [First]   1 [Yes]  0.917 152.  0 [Male]  
3 1 [First]   0 [No]   2     152.  1 [Female]
4 1 [First]   0 [No]  30     152.  0 [Male]  
5 1 [First]   0 [No]  25     152.  1 [Female]
6 1 [First]   1 [Yes] 48      26.6 0 [Male]  

attributes(titanic$pclass)

$label
[1] "Passenger Class"

$format.spss
[1] "F8.0"

$class
[1] "haven_labelled"

$labels
 First Second  Third 
     1      2      3 

Read and combine many files

• There are 8 MS-Excel files with the same structure in a folder
• Each has 10 observations on two variables, X and Y
• First, I load the package needed for reading Excel files, then get a list of the file names

library(openxlsx)
my.files <- list.files("c:/chuck/NYU/Stat Group/R Workshop/Many Files/", 
                       pattern = ".xlsx$", full.names=TRUE, recursive=TRUE)
my.files # vector of the file names with full path

[1] "c:/chuck/NYU/Stat Group/R Workshop/Many Files/File1.xlsx"
[2] "c:/chuck/NYU/Stat Group/R Workshop/Many Files/File2.xlsx"
[3] "c:/chuck/NYU/Stat Group/R Workshop/Many Files/File3.xlsx"
[4] "c:/chuck/NYU/Stat Group/R Workshop/Many Files/File4.xlsx"
[5] "c:/chuck/NYU/Stat Group/R Workshop/Many Files/File5.xlsx"
[6] "c:/chuck/NYU/Stat Group/R Workshop/Many Files/File6.xlsx"
[7] "c:/chuck/NYU/Stat Group/R Workshop/Many Files/File7.xlsx"
[8] "c:/chuck/NYU/Stat Group/R Workshop/Many Files/File8.xlsx"

• Next I gather the names of the worksheets within each workbook

my.sheets <- lapply(my.files, function(x){getSheetNames(x)}) # list of worksheet names 
                                                             # within each MS-Excel workbook
unlist(my.sheets)

[1] "Sheet 1" "Sheet 1" "Sheet 1" "Sheet 1" "Sheet 1" "Sheet 1" "Sheet 1"
[8] "Sheet 1"

• I put the workbook filenames and worksheet names together in a data frame

my.sheets.DF <- data.frame(file = rep(my.files, unlist(lapply(my.sheets, length))), sheet = unlist(my.sheets))
my.sheets.DF

                                                      file   sheet
1 c:/chuck/NYU/Stat Group/R Workshop/Many Files/File1.xlsx Sheet 1
2 c:/chuck/NYU/Stat Group/R Workshop/Many Files/File2.xlsx Sheet 1
3 c:/chuck/NYU/Stat Group/R Workshop/Many Files/File3.xlsx Sheet 1
4 c:/chuck/NYU/Stat Group/R Workshop/Many Files/File4.xlsx Sheet 1
5 c:/chuck/NYU/Stat Group/R Workshop/Many Files/File5.xlsx Sheet 1
6 c:/chuck/NYU/Stat Group/R Workshop/Many Files/File6.xlsx Sheet 1
7 c:/chuck/NYU/Stat Group/R Workshop/Many Files/File7.xlsx Sheet 1
8 c:/chuck/NYU/Stat Group/R Workshop/Many Files/File8.xlsx Sheet 1

• I create an empty list to hold each data file

my.list <- vector(mode="list", length = nrow(my.sheets.DF)) # empty list to hold each data file

• I loop over the file and worksheet names, reading each in and putting it into the list

for(i in 1:nrow(my.sheets.DF)){
  my.list[[i]] <- read.xlsx(xlsxFile = as.character(my.sheets.DF$file)[i], 
                            sheet = as.character(my.sheets.DF$sheet)[i])  
}

• Finally, I combine the 8 data frames into one big data frame

my.DF <- as.data.frame(do.call(rbind, my.list))
dim(my.DF) # 80 observations, 2 variables 

[1] 80  2

• The example has just 8 files in the folder, but it could be thousands and the principle is the same

Getting data out of R

• write.table for plain text (comma or tab delimited)
• write_sav for SPSS (haven package)
• write_dta for Stata (haven package)
• write.xlsx for MS-Excel (openxlsx package)

Data management

Recoding

library(car)
auto <- read_sav("c:/chuck/NYU/Stat Group/R Workshop/auto.sav")
summary(auto$MPG)
auto$MPG3 <- car::recode(auto$MPG, "lo:18=1; 19:23=2; 24:hi=3")

table(auto$MPG3)

 1  2  3 
27 24 23 

Merging

Two data frames with a common ID variable

A <- data.frame(famid = c(2,1,3), 
                name = c('Art','Bill','Paul'), 
                inc = c(22,30,25))
B <- data.frame(famid = c(3,1,2), 
                faminc96 = c(75,40,45), 
                faminc97 = c(76,40.5,40.4), 
                faminc98 = c(77,41,45.8))
intersect(names(A), names(B))

[1] "famid"

One Merged Data Frame

A

  famid name inc
1     2  Art  22
2     1 Bill  30
3     3 Paul  25

B

  famid faminc96 faminc97 faminc98
1     3       75     76.0     77.0
2     1       40     40.5     41.0
3     2       45     40.4     45.8

AB <- merge(A, B)
AB

  famid name inc faminc96 faminc97 faminc98
1     1 Bill  30       40     40.5     41.0
2     2  Art  22       45     40.4     45.8
3     3 Paul  25       75     76.0     77.0

Subsetting

bank <- read_sav("c:/chuck/NYU/Stat Group/bank.sav")
bank <- as_factor(bank)
head(bank)

# A tibble: 6 x 19
     ID SALBEG SEX    TIME   AGE SALNOW EDLEVEL  WORK JOBCAT MINORITY SEXRACE
  <dbl>  <dbl> <fct> <dbl> <dbl>  <dbl>   <dbl> <dbl> <fct>  <fct>    <fct>  
1   628   8400 Males    81  28.5  16080      16  0.25 Colle… White    White …
2   630  24000 Males    73  40.3  41400      16 12.5  Exemp… White    White …
3   632  10200 Males    83  31.1  21960      15  4.08 Exemp… White    White …
4   633   8700 Males    93  31.2  19200      16  1.83 Colle… White    White …
5   635  17400 Males    83  41.9  28350      19 13    Exemp… White    White …
6   637  12996 Males    80  29.5  27250      18  2.42 Colle… White    White …
# … with 8 more variables: EGENDER <dbl>, EMINORIT <dbl>, EGENXMIN <dbl>,
#   BSALCENT <dbl>, CSALADJ <dbl>, SALDELTA <dbl>, RES_1 <dbl>, GENDER <fct>

• The head() function is a convenient way to see the first few observations of a data object

• With the subset() function

subset(bank, SALBEG < 4000 & SEX == "Males", select=c(ID,SEX,SALBEG,AGE,SALNOW))

# A tibble: 2 x 5
     ID SEX   SALBEG   AGE SALNOW
  <dbl> <fct>  <dbl> <dbl>  <dbl>
1   926 Males   3600  53.5  12300
2  1077 Males   3900  29.2   9000

• Or by indexing

bank[bank$SALBEG < 4000 & bank$SEX == "Males", c(1,3,2,5,6)]

# A tibble: 2 x 5
     ID SEX   SALBEG   AGE SALNOW
  <dbl> <fct>  <dbl> <dbl>  <dbl>
1   926 Males   3600  53.5  12300
2  1077 Males   3900  29.2   9000

• In both cases, I selected males with a beginning salary less than 4000, and only certain variables
  • subset specified the variables to include by name
  • indexing specified the variables to include based on their location in the data frame

Reshaping, Wide to Long

mytable <- read.table("c:/chuck/NYU/Stat Group/table1.txt", sep=",", header=TRUE)
mytable

  id female inc80 inc81 inc82
1  1      0  5000  5500  6000
2  2      1  2000  2200  3300
3  3      0  3000  2000  1000

library(dplyr)
library(tidyr)
longtab <- gather(mytable, year, inc, inc80:inc82)
longtab

  id female  year  inc
1  1      0 inc80 5000
2  2      1 inc80 2000
3  3      0 inc80 3000
4  1      0 inc81 5500
5  2      1 inc81 2200
6  3      0 inc81 2000
7  1      0 inc82 6000
8  2      1 inc82 3300
9  3      0 inc82 1000

Reshaping, Long to Wide

longtab

  id female  year  inc
1  1      0 inc80 5000
2  2      1 inc80 2000
3  3      0 inc80 3000
4  1      0 inc81 5500
5  2      1 inc81 2200
6  3      0 inc81 2000
7  1      0 inc82 6000
8  2      1 inc82 3300
9  3      0 inc82 1000

widetab <- spread(longtab, year, inc)
widetab

  id female inc80 inc81 inc82
1  1      0  5000  5500  6000
2  2      1  2000  2200  3300
3  3      0  3000  2000  1000

Reshaping with data.table

• https://cran.r-project.org/web/packages/data.table/vignettes/datatable-reshape.html
• https://github.com/Rdatatable/data.table/wiki/Getting-started

Aggregating

head(iris)

  Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1          5.1         3.5          1.4         0.2  setosa
2          4.9         3.0          1.4         0.2  setosa
3          4.7         3.2          1.3         0.2  setosa
4          4.6         3.1          1.5         0.2  setosa
5          5.0         3.6          1.4         0.2  setosa
6          5.4         3.9          1.7         0.4  setosa

aggregate(iris[,1:4], list(Species = iris$Species), FUN = mean)

     Species Sepal.Length Sepal.Width Petal.Length Petal.Width
1     setosa        5.006       3.428        1.462       0.246
2 versicolor        5.936       2.770        4.260       1.326
3  virginica        6.588       2.974        5.552       2.026

Set Operations

x <- c('A','B','C','D')
y <- c('D','A','F','J')
setdiff(x, y) # which elements of x are not in y

[1] "B" "C"

setdiff(y, x) # which elements of y are not in x

[1] "F" "J"

intersect(x, y) # what elements are in both x and y

[1] "A" "D"

union(x, y) # elements in either x or y

[1] "A" "B" "C" "D" "F" "J"

"C" %in% x # is there a "C" in x

[1] TRUE

y %in% c("F","J") # which elements of y are equal to "F" or "J"

[1] FALSE FALSE  TRUE  TRUE

Character Manipulation

x <- c('A','B','C','D')
grep('C', x)

[1] 3

gsub('C', 'c', x)

[1] "A" "B" "c" "D"

paste('Item', 1:10, sep="-")

 [1] "Item-1"  "Item-2"  "Item-3"  "Item-4"  "Item-5"  "Item-6"  "Item-7" 
 [8] "Item-8"  "Item-9"  "Item-10"

x <- c('fruit_apple','instrument_guitar','instrument_piano','fruit_orange','instrument_trumpet')
grepl("fruit", x)

[1]  TRUE FALSE FALSE  TRUE FALSE

dplyr package

• library(dplyr)
• filter()
• select()
• mutate()
• summarize()
• group_by()
• arrange()

Houston flights data

• All flights departing from Houston airports IAH and HOU
• Research and Innovation Technology Administration at the Bureau of Transporation Statistics

library(hflights)
head(hflights)

     Year Month DayofMonth DayOfWeek DepTime ArrTime UniqueCarrier FlightNum
5424 2011     1          1         6    1400    1500            AA       428
5425 2011     1          2         7    1401    1501            AA       428
5426 2011     1          3         1    1352    1502            AA       428
5427 2011     1          4         2    1403    1513            AA       428
5428 2011     1          5         3    1405    1507            AA       428
5429 2011     1          6         4    1359    1503            AA       428
     TailNum ActualElapsedTime AirTime ArrDelay DepDelay Origin Dest Distance
5424  N576AA                60      40      -10        0    IAH  DFW      224
5425  N557AA                60      45       -9        1    IAH  DFW      224
5426  N541AA                70      48       -8       -8    IAH  DFW      224
5427  N403AA                70      39        3        3    IAH  DFW      224
5428  N492AA                62      44       -3        5    IAH  DFW      224
5429  N262AA                64      45       -7       -1    IAH  DFW      224
     TaxiIn TaxiOut Cancelled CancellationCode Diverted
5424      7      13         0                         0
5425      6       9         0                         0
5426      5      17         0                         0
5427      9      22         0                         0
5428      9       9         0                         0
5429      6      13         0                         0

str(hflights)

'data.frame':   227496 obs. of  21 variables:
 $ Year             : int  2011 2011 2011 2011 2011 2011 2011 2011 2011 2011 ...
 $ Month            : int  1 1 1 1 1 1 1 1 1 1 ...
 $ DayofMonth       : int  1 2 3 4 5 6 7 8 9 10 ...
 $ DayOfWeek        : int  6 7 1 2 3 4 5 6 7 1 ...
 $ DepTime          : int  1400 1401 1352 1403 1405 1359 1359 1355 1443 1443 ...
 $ ArrTime          : int  1500 1501 1502 1513 1507 1503 1509 1454 1554 1553 ...
 $ UniqueCarrier    : chr  "AA" "AA" "AA" "AA" ...
 $ FlightNum        : int  428 428 428 428 428 428 428 428 428 428 ...
 $ TailNum          : chr  "N576AA" "N557AA" "N541AA" "N403AA" ...
 $ ActualElapsedTime: int  60 60 70 70 62 64 70 59 71 70 ...
 $ AirTime          : int  40 45 48 39 44 45 43 40 41 45 ...
 $ ArrDelay         : int  -10 -9 -8 3 -3 -7 -1 -16 44 43 ...
 $ DepDelay         : int  0 1 -8 3 5 -1 -1 -5 43 43 ...
 $ Origin           : chr  "IAH" "IAH" "IAH" "IAH" ...
 $ Dest             : chr  "DFW" "DFW" "DFW" "DFW" ...
 $ Distance         : int  224 224 224 224 224 224 224 224 224 224 ...
 $ TaxiIn           : int  7 6 5 9 9 6 12 7 8 6 ...
 $ TaxiOut          : int  13 9 17 22 9 13 15 12 22 19 ...
 $ Cancelled        : int  0 0 0 0 0 0 0 0 0 0 ...
 $ CancellationCode : chr  "" "" "" "" ...
 $ Diverted         : int  0 0 0 0 0 0 0 0 0 0 ...

Using filter() to select observations

• January flights by American Airlines

head(filter(hflights, Month == 1, UniqueCarrier == "AA"))

  Year Month DayofMonth DayOfWeek DepTime ArrTime UniqueCarrier FlightNum
1 2011     1          1         6    1400    1500            AA       428
2 2011     1          2         7    1401    1501            AA       428
3 2011     1          3         1    1352    1502            AA       428
4 2011     1          4         2    1403    1513            AA       428
5 2011     1          5         3    1405    1507            AA       428
6 2011     1          6         4    1359    1503            AA       428
  TailNum ActualElapsedTime AirTime ArrDelay DepDelay Origin Dest Distance
1  N576AA                60      40      -10        0    IAH  DFW      224
2  N557AA                60      45       -9        1    IAH  DFW      224
3  N541AA                70      48       -8       -8    IAH  DFW      224
4  N403AA                70      39        3        3    IAH  DFW      224
5  N492AA                62      44       -3        5    IAH  DFW      224
6  N262AA                64      45       -7       -1    IAH  DFW      224
  TaxiIn TaxiOut Cancelled CancellationCode Diverted
1      7      13         0                         0
2      6       9         0                         0
3      5      17         0                         0
4      9      22         0                         0
5      9       9         0                         0
6      6      13         0                         0

Using select() to select variables

• Just the Departure Time, Arrival Time, and Air Time variables

head(select(hflights, DepTime, ArrTime, AirTime))

     DepTime ArrTime AirTime
5424    1400    1500      40
5425    1401    1501      45
5426    1352    1502      48
5427    1403    1513      39
5428    1405    1507      44
5429    1359    1503      45

• All variables that end with Time

head(select(hflights, ends_with("Time")))

     DepTime ArrTime ActualElapsedTime AirTime
5424    1400    1500                60      40
5425    1401    1501                60      45
5426    1352    1502                70      48
5427    1403    1513                70      39
5428    1405    1507                62      44
5429    1359    1503                64      45

Using mutate() to create new variables

g1 <- mutate(hflights, ActualGroundTime = ActualElapsedTime - AirTime)
head(select(g1, ActualElapsedTime, AirTime, ActualGroundTime))

  ActualElapsedTime AirTime ActualGroundTime
1                60      40               20
2                60      45               15
3                70      48               22
4                70      39               31
5                62      44               18
6                64      45               19

Using summarize()

summarize(hflights, min_dist = min(Distance),
                    mean_dist = mean(Distance),
                    median_dist = median(Distance),
                    sd_dist = sd(Distance),
                    max_dist = max(Distance))

  min_dist mean_dist median_dist  sd_dist max_dist
1       79  787.7832         809 453.6806     3904

Using group_by() and summarize() to summarize by group

• This also illustrates the use of pipes in R

hflights %>% group_by(UniqueCarrier) %>%
summarize(min_dist = min(Distance),
          mean_dist = mean(Distance),
          median_dist = median(Distance),
          sd_dist = sd(Distance),
          max_dist = max(Distance))

# A tibble: 15 x 6
   UniqueCarrier min_dist mean_dist median_dist sd_dist max_dist
   <chr>            <int>     <dbl>       <dbl>   <dbl>    <int>
 1 AA                 224      484.         224  353.        964
 2 AS                1874     1874         1874    0        1874
 3 B6                1428     1428         1428    0        1428
 4 CO                 140     1098.        1190  505.       3904
 5 DL                 689      723.         689  104.       1076
 6 EV                 468      776.         696  260.       1076
 7 F9                 666      883.         883    7.50      883
 8 FL                 490      685.         696   45.5       696
 9 MQ                 247      651.         247  448.       1379
10 OO                 140      820.         809  300.       1428
11 UA                 643     1178.         925  326.       1635
12 US                 912      981.         913  110.       1325
13 WN                 148      607.         453  399.       1642
14 XE                  79      589.         562  281.       1201
15 YV                 912      939.         913   79.6      1190

• Notice group_by() and summarize() essentially aggregate

iris %>% 
  group_by(Species) %>%
  summarize(Sepal.Length = mean(Sepal.Length),
            Sepal.Width = mean(Sepal.Width),
            Petal.Length = mean(Petal.Length),
            Petal.Width = mean(Petal.Width))

# A tibble: 3 x 5
  Species    Sepal.Length Sepal.Width Petal.Length Petal.Width
  <fct>             <dbl>       <dbl>        <dbl>       <dbl>
1 setosa             5.01        3.43         1.46       0.246
2 versicolor         5.94        2.77         4.26       1.33 
3 virginica          6.59        2.97         5.55       2.03 

• But much more flexibly!

Putting data into a desired order with arrange()

hflights %>% group_by(UniqueCarrier) %>%
summarize(min_dist = min(Distance),
          mean_dist = mean(Distance),
          median_dist = median(Distance),
          sd_dist = sd(Distance),
          max_dist = max(Distance)) %>%
arrange(mean_dist)

# A tibble: 15 x 6
   UniqueCarrier min_dist mean_dist median_dist sd_dist max_dist
   <chr>            <int>     <dbl>       <dbl>   <dbl>    <int>
 1 AA                 224      484.         224  353.        964
 2 XE                  79      589.         562  281.       1201
 3 WN                 148      607.         453  399.       1642
 4 MQ                 247      651.         247  448.       1379
 5 FL                 490      685.         696   45.5       696
 6 DL                 689      723.         689  104.       1076
 7 EV                 468      776.         696  260.       1076
 8 OO                 140      820.         809  300.       1428
 9 F9                 666      883.         883    7.50      883
10 YV                 912      939.         913   79.6      1190
11 US                 912      981.         913  110.       1325
12 CO                 140     1098.        1190  505.       3904
13 UA                 643     1178.         925  326.       1635
14 B6                1428     1428         1428    0        1428
15 AS                1874     1874         1874    0        1874

Benefits of Piping

Without Piping

arrange(
  summarize(
    group_by(
      filter(mtcars, carb > 1),
    cyl),
  Avg_mpg = mean(mpg)
  ),
desc(Avg_mpg)  
  )

# A tibble: 3 x 2
    cyl Avg_mpg
  <dbl>   <dbl>
1     4    25.9
2     6    19.7
3     8    15.1

With Piping

mtcars %>%
  filter(carb > 1) %>%
  group_by(cyl) %>%
  summarize(Avg_mpg = mean(mpg)) %>%
  arrange(desc(Avg_mpg))

# A tibble: 3 x 2
    cyl Avg_mpg
  <dbl>   <dbl>
1     4    25.9
2     6    19.7
3     8    15.1

Plots

Histogram

hsb2 <- read_sav("https://clelandcm.github.io/Hands-On-R-Practice/hsb2.sav")
library(ggplot2)
ggplot(hsb2, aes(x = WRITE)) + geom_histogram(color = "grey", fill = "#34ebbd")

Bar

library(openxlsx)
fname <- read.xlsx("c:/chuck/NYU/Stat Group/R Workshop/Female-Names.xlsx", sheet = 1)
fname

   Rank      Name Ngirls
1     1      Emma  20799
2     2    Olivia  19674
3     3    Sophia  18490
4     4  Isabella  16950
5     5       Ava  15586
6     6       Mia  13442
7     7     Emily  12562
8     8   Abigail  11985
9     9   Madison  10247
10   10 Charlotte  10048

ggplot(fname, aes(x = forcats::fct_reorder(Name, Ngirls), y = Ngirls)) + 
  geom_bar(stat = 'identity') + 
  ylab('Number') + xlab('') + 
  ggtitle('Ten Most Common Female Baby\nNames in 2014') +
  theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1))

Scatter

ggplot2 package

ggplot(hsb2, aes(x = WRITE, y = READ)) + geom_point()

Base R

plot(READ ~ WRITE, data = hsb2)

Scatter Enhanced

library(ggplot2)
bank$GENDER <- as_factor(bank$GENDER)
ggplot(subset(bank, SALNOW < 30000), aes(x = SALBEG, y = SALNOW, color = GENDER)) + 
  geom_point()

Scatter with Facets

library(ggplot2)
ggplot(subset(bank, SALNOW < 30000), aes(x = SALBEG, y = SALNOW)) + 
  geom_point() + 
  facet_wrap( ~ GENDER)

Boxplots

• Writing score on vertical axis

hsb <- read_dta('c:/chuck/NYU/Stat Group/R Workshop/hsb.dta')
hsb <- as_factor(hsb)
ggplot(hsb, aes(x = female, y = write)) + geom_boxplot() + xlab("") +
  theme(axis.text = element_text(size = 4),
        axis.title = element_text(size = 5))

• Flip coordinates so writing score is on the horizontal axis

ggplot(hsb, aes(x = female, y = write)) + geom_boxplot() + xlab("") + coord_flip()

Alpha Transparency

• Without transparency

ggplot(myDF, aes(x=X,y=Y)) + geom_point(color="blue", size=3)

• With transparency

ggplot(myDF, aes(x=X,y=Y)) + geom_point(color="blue", size=3, alpha =.20)

Networks

library(igraph)
net.bg <- barabasi.game(80) 
V(net.bg)$frame.color <- sample(c("white","black"), size = 80, replace=TRUE, prob=c(0.5,0.5))
V(net.bg)$color <- sample(c("orange","lightblue"), size = 80, replace=TRUE, prob=c(0.5,0.5))
V(net.bg)$label <- "" 
V(net.bg)$size <- 10
E(net.bg)$arrow.mode <- 0
plot(net.bg, layout=layout.lgl)

A more customized plot

library(ggplot2) # devtools::install_github("hadley/ggplot2")
library(ggalt)   # devtools::install_github("hrbrmstr/ggalt")
library(dplyr)   # for data_frame() & arrange()

df <- data_frame(country=c("Germany", "France", "Vietnam", "Japan", "Poland", "Lebanon",
                           "Australia", "South\nKorea", "Canada", "Spain", "Italy", "Peru",
                           "U.S.", "UK", "Mexico", "Chile", "China", "India"),
                 ages_35=c(0.39, 0.42, 0.49, 0.43, 0.51, 0.57,
                           0.60, 0.45, 0.65, 0.57, 0.57, 0.65,
                           0.63, 0.59, 0.67, 0.75, 0.52, 0.48),
                 ages_18_to_34=c(0.81, 0.83, 0.86, 0.78, 0.86, 0.90,
                                 0.91, 0.75, 0.93, 0.85, 0.83, 0.91,
                                 0.89, 0.84, 0.90, 0.96, 0.73, 0.69),
                 diff=sprintf("+%d", as.integer((ages_18_to_34-ages_35)*100)))

df <- arrange(df, desc(diff))
df$country <- factor(df$country, levels=rev(df$country))

percent_first <- function(x) {
  x <- sprintf("%d%%", round(x*100))
  x[2:length(x)] <- sub("%$", "", x[2:length(x)])
  x
}

gg <- ggplot()
gg <- gg + geom_segment(data=df, aes(y=country, yend=country, x=0, xend=1), color="#b2b2b2", size=0.15)
gg <- gg + geom_segment(data=df, aes(y=country, yend=country, x=ages_35, xend=ages_18_to_34), color="#b2b2b2", size=2)
gg <- gg + geom_point(data=df, aes(x=ages_35, y = country), size=3, colour = "#9fb059")
gg <- gg + geom_point(data=df, aes(x=ages_18_to_34, y = country), size=3, colour = "#edae52")
gg <- gg + geom_text(data=dplyr::filter(df, country=="Germany"),
                     aes(x=ages_35, y=country, label="Ages 35+"),
                     color="#9fb059", size=3, vjust=-1, fontface="bold", family="Calibri")
gg <- gg + geom_text(data=dplyr::filter(df, country=="Germany"),
                     aes(x=ages_18_to_34, y=country, label="Ages 18-34"),
                     color="#edae52", size=3, vjust=-1, fontface="bold", family="Calibri")
gg <- gg + geom_text(data=df, aes(x=ages_35, y=country, label=percent_first(ages_35)),
                     color="#9fb059", size=2.75, vjust=1.75, family="Calibri")
gg <- gg + geom_text(data=df, color="#edae52", size=2.75, vjust=1.75, family="Calibri",
                     aes(x=ages_18_to_34, y=country, label=percent_first(ages_18_to_34)))
gg <- gg + geom_rect(data=df, aes(xmin=1.05, xmax=1.175, ymin=-Inf, ymax=Inf), fill="#efefe3")
gg <- gg + geom_text(data=df, aes(label=diff, y=country, x=1.1125), fontface="bold", size=3, family="Calibri")
gg <- gg + geom_text(data=filter(df, country=="Germany"), aes(x=1.1125, y=country, label="DIFF"),
                     color="#7a7d7e", size=3.1, vjust=-2, fontface="bold", family="Calibri")
gg <- gg + scale_x_continuous(expand=c(0,0), limits=c(0, 1.175))
gg <- gg + scale_y_discrete(expand=c(0.075,0))
gg <- gg + labs(x=NULL, y=NULL, title="The social media age gap",
                subtitle="Adult internet users or reported smartphone owners who\nuse social networking sites",
                caption="Source: Pew Research Center, Spring 2015 Global Attitudes Survey. Q74")
gg <- gg + theme_bw(base_family="Calibri")
gg <- gg + theme(panel.grid.major=element_blank())
gg <- gg + theme(panel.grid.minor=element_blank())
gg <- gg + theme(panel.border=element_blank())
gg <- gg + theme(axis.ticks=element_blank())
gg <- gg + theme(axis.text.x=element_blank())
gg <- gg + theme(plot.title=element_text(face="bold"))
gg <- gg + theme(plot.subtitle=element_text(face="italic", size=9, margin=margin(b=12)))
gg <- gg + theme(plot.caption=element_text(size=7, margin=margin(t=12), color="#7a7d7e"))
gg

Analysis

descriptive statistics

hsb <- read_dta('c:/chuck/NYU/Stat Group/R Workshop/hsb.dta')
summary(hsb)

       id             female           race           ses            schtyp    
 Min.   :  1.00   Min.   :0.000   Min.   :1.00   Min.   :1.000   Min.   :1.00  
 1st Qu.: 50.75   1st Qu.:0.000   1st Qu.:3.00   1st Qu.:2.000   1st Qu.:1.00  
 Median :100.50   Median :1.000   Median :4.00   Median :2.000   Median :1.00  
 Mean   :100.50   Mean   :0.545   Mean   :3.43   Mean   :2.055   Mean   :1.16  
 3rd Qu.:150.25   3rd Qu.:1.000   3rd Qu.:4.00   3rd Qu.:3.000   3rd Qu.:1.00  
 Max.   :200.00   Max.   :1.000   Max.   :4.00   Max.   :3.000   Max.   :2.00  
      prog            read           write            math      
 Min.   :1.000   Min.   :28.00   Min.   :31.00   Min.   :33.00  
 1st Qu.:2.000   1st Qu.:44.00   1st Qu.:45.75   1st Qu.:45.00  
 Median :2.000   Median :50.00   Median :54.00   Median :52.00  
 Mean   :2.025   Mean   :52.23   Mean   :52.77   Mean   :52.65  
 3rd Qu.:2.250   3rd Qu.:60.00   3rd Qu.:60.00   3rd Qu.:59.00  
 Max.   :3.000   Max.   :76.00   Max.   :67.00   Max.   :75.00  
    science          socst      
 Min.   :26.00   Min.   :26.00  
 1st Qu.:44.00   1st Qu.:46.00  
 Median :53.00   Median :52.00  
 Mean   :51.85   Mean   :52.41  
 3rd Qu.:58.00   3rd Qu.:61.00  
 Max.   :74.00   Max.   :71.00  

frequencies

library(descr)
with(bank, freq(JOBCAT, plot=FALSE))

Employment category 
                 Frequency Percent
Clerical               227  47.890
Office trainee         136  28.692
Security officer        27   5.696
College trainee         41   8.650
Exempt employee         32   6.751
MBA trainee              5   1.055
Technical                6   1.266
Total                  474 100.000

crosstabulation

library(descr)
with(bank, CrossTable(SEX, JOBCAT %in% c("Clerical","Office trainee"), 
                    prop.r=TRUE, prop.chi=FALSE, prop.t=FALSE, prop.c=FALSE, chisq=TRUE))

.    Cell Contents 
. |-------------------------|
. |                   Count | 
. |             Row Percent | 
. |-------------------------|
. 
. ========================================
.                    JOBCAT %in% c("Clerical", "Office trainee")
. Sex of employee    FALSE    TRUE   Total
. ----------------------------------------
. Males               101     157     258 
.                    39.1%   60.9%   54.4%
. ----------------------------------------
. Females              10     206     216 
.                     4.6%   95.4%   45.6%
. ----------------------------------------
. Total               111     363     474 
. ========================================
. 
. Statistics for All Table Factors
. 
. Pearson's Chi-squared test 
. ------------------------------------------------------------
. Chi^2 = 78.10967      d.f. = 1      p <2e-16 
. 
. Pearson's Chi-squared test with Yates' continuity correction 
. ------------------------------------------------------------
. Chi^2 = 76.19681      d.f. = 1      p <2e-16 
.         Minimum expected frequency: 50.58228

More detailed descriptive statistics for quantitative variables

library(psych)
psych::describe(subset(hsb, select=c(read,write,math,science,socst)))

        vars   n  mean    sd median trimmed   mad min max range  skew kurtosis
read       1 200 52.23 10.25     50   52.03 10.38  28  76    48  0.19    -0.66
write      2 200 52.77  9.48     54   53.36 11.86  31  67    36 -0.47    -0.78
math       3 200 52.65  9.37     52   52.23 10.38  33  75    42  0.28    -0.69
science    4 200 51.85  9.90     53   52.02 11.86  26  74    48 -0.19    -0.60
socst      5 200 52.41 10.74     52   52.99 13.34  26  71    45 -0.38    -0.57
          se
read    0.72
write   0.67
math    0.66
science 0.70
socst   0.76

t-tests

• Following these examples: http://www.ats.ucla.edu/stat/stata/output/ttest_output.htm
• One sample t-test where hypothesized mean for write score is 50

hsb <- read_dta('c:/chuck/NYU/Stat Group/R Workshop/hsb.dta')
with(hsb, t.test(write, mu=50))

    One Sample t-test

data:  write
t = 4.1403, df = 199, p-value = 5.121e-05
alternative hypothesis: true mean is not equal to 50
95 percent confidence interval:
 51.45332 54.09668
sample estimates:
mean of x 
   52.775 

• Paired t-test comparing read and write scores

with(hsb, t.test(write, read, paired = TRUE))

    Paired t-test

data:  write and read
t = 0.86731, df = 199, p-value = 0.3868
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -0.6941424  1.7841424
sample estimates:
mean of the differences 
                  0.545 

• Independent-samples t-test comparing write scores of male and female students

t.test(write ~ female, data = hsb, var.equal = TRUE)

    Two Sample t-test

data:  write by female
t = -3.7341, df = 198, p-value = 0.0002463
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -7.441835 -2.298059
sample estimates:
mean in group 0 mean in group 1 
       50.12088        54.99083 

• Do not assume equal variance in each group

t.test(write ~ female, data = hsb)

    Welch Two Sample t-test

data:  write by female
t = -3.6564, df = 169.71, p-value = 0.0003409
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -7.499159 -2.240734
sample estimates:
mean in group 0 mean in group 1 
       50.12088        54.99083 

Correlation

hsb <- read_sav("c:/chuck/NYU/Stat Group/R Workshop/hsb2.sav")
round(cor(subset(hsb, select=c(READ,WRITE,MATH,SCIENCE,SOCST))), 2)

        READ WRITE MATH SCIENCE SOCST
READ    1.00  0.60 0.66    0.63  0.62
WRITE   0.60  1.00 0.62    0.57  0.60
MATH    0.66  0.62 1.00    0.63  0.54
SCIENCE 0.63  0.57 0.63    1.00  0.47
SOCST   0.62  0.60 0.54    0.47  1.00

cor.test(~ READ + SOCST, data = hsb)

    Pearson's product-moment correlation

data:  READ and SOCST
t = 11.163, df = 198, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 0.5282957 0.6998781
sample estimates:
      cor 
0.6214843 

Linear Regression

• Following this SPSS example: https://stats.idre.ucla.edu/spss/output/regression-analysis/

hsb <- read_sav("c:/chuck/NYU/Stat Group/R Workshop/hsb2.sav")
head(hsb)

# A tibble: 6 x 11
     ID   FEMALE    RACE     SES  SCHTYP    PROG  READ WRITE  MATH SCIENCE SOCST
  <dbl> <dbl+lb> <dbl+l> <dbl+l> <dbl+l> <dbl+l> <dbl> <dbl> <dbl>   <dbl> <dbl>
1    70 0 [male] 4 [whi… 1 [low] 1 [pub… 1 [gen…    57    52    41      47    57
2   121 1 [fema… 4 [whi… 2 [mid… 1 [pub… 3 [voc…    68    59    53      63    61
3    86 0 [male] 4 [whi… 3 [hig… 1 [pub… 1 [gen…    44    33    54      58    31
4   141 0 [male] 4 [whi… 3 [hig… 1 [pub… 3 [voc…    63    44    47      53    56
5   172 0 [male] 4 [whi… 2 [mid… 1 [pub… 2 [aca…    47    52    57      53    61
6   113 0 [male] 4 [whi… 2 [mid… 1 [pub… 2 [aca…    44    52    51      63    61

• Do the multiple regression analysis using the R lm() function (for linear model)

lm.1 <- lm(SCIENCE ~ MATH + FEMALE + SOCST + READ, data = hsb)

• Summarize the fitted model

summary(lm.1)

Call:
lm(formula = SCIENCE ~ MATH + FEMALE + SOCST + READ, data = hsb)

Residuals:
     Min       1Q   Median       3Q      Max 
-18.6706  -4.5764  -0.3237   4.5006  21.8563 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept) 12.32529    3.19356   3.859 0.000154 ***
MATH         0.38931    0.07412   5.252 3.92e-07 ***
FEMALE      -2.00976    1.02272  -1.965 0.050820 .  
SOCST        0.04984    0.06223   0.801 0.424139    
READ         0.33530    0.07278   4.607 7.36e-06 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 7.148 on 195 degrees of freedom
Multiple R-squared:  0.4892,    Adjusted R-squared:  0.4788 
F-statistic: 46.69 on 4 and 195 DF,  p-value: < 2.2e-16

• Confidence intervals

confint(lm.1)

                  2.5 %      97.5 %
(Intercept)  6.02694246 18.62363584
MATH         0.24312201  0.53549835
FEMALE      -4.02677214  0.00724283
SOCST       -0.07288986  0.17257843
READ         0.19176512  0.47883447

Logistic Regression

• Following this SPSS example: https://stats.idre.ucla.edu/spss/examples/alr2/applied-logistic-regression-second-edition-by-hosmer-and-lemeshowchapter-2-multiple-logistic-regression/
• Chapter 2, Applied Logistic Regression, Second Edition, by Hosmer and Lemeshow

Variable	Description	Codes/Values
LOW	Low Birth Weight	1 = BWT<=2500g, 0 = BWT>2500g
AGE	Age of Mother	Years
LWT	Weight of Mother at Last Menstrual Period	Pounds
RACE	Race	1=White, 2=Black, 3=Other
FTV	First Trimester Physician Visits	0=None, 1=One, 2=Two,etc.

• R has a function, glm(), for generalized linear models, and logistic regression is a special case of generalized linear models
• This is similar to the functionality of PROC GENMOD in SAS
• Before modeling, we will read in the data and convert some variables to factors

lowbwt <- read_sav('c:/chuck/NYU/Stat Group/R Workshop/lowbwt.sav')
lowbwt$RACE <- car::recode(lowbwt$RACE, "1='White';2='Black';3='Other'", as.factor = TRUE)
lowbwt$RACE <- relevel(lowbwt$RACE, ref = 'White')

• And now do the logistic regression

lrm.1 <- glm(LOW ~ AGE + LWT + RACE + FTV, family='binomial', data = lowbwt)

• Summarize it

summary(lrm.1)

Call:
glm(formula = LOW ~ AGE + LWT + RACE + FTV, family = "binomial", 
    data = lowbwt)

Deviance Residuals: 
    Min       1Q   Median       3Q      Max  
-1.4163  -0.8931  -0.7113   1.2454   2.0755  

Coefficients:
             Estimate Std. Error z value Pr(>|z|)  
(Intercept)  1.295366   1.071443   1.209   0.2267  
AGE         -0.023823   0.033730  -0.706   0.4800  
LWT         -0.014245   0.006541  -2.178   0.0294 *
RACEBlack    1.003898   0.497859   2.016   0.0438 *
RACEOther    0.433108   0.362240   1.196   0.2318  
FTV         -0.049308   0.167239  -0.295   0.7681  
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

(Dispersion parameter for binomial family taken to be 1)

    Null deviance: 234.67  on 188  degrees of freedom
Residual deviance: 222.57  on 183  degrees of freedom
AIC: 234.57

Number of Fisher Scoring iterations: 4

• Odds ratios and confidence intervals

exp(coef(lrm.1)[-1]) # Removing constant

      AGE       LWT RACEBlack RACEOther       FTV 
0.9764586 0.9858564 2.7288979 1.5420434 0.9518876 

exp(confint(lrm.1)[-1,]) # Removing constant from confidence intervals too

              2.5 %    97.5 %
AGE       0.9124232 1.0421301
LWT       0.9725636 0.9979524
RACEBlack 1.0232217 7.3225967
RACEOther 0.7567464 3.1462285
FTV       0.6771508 1.3109248

Extracting Data from Google Scholar

library(scholar)
library(purrr)

DF <- data.frame(Person = c("Chuck Cleland","Sam Friedman","Holly Hagan","Dani Ompad"),
                 GID = c("AuiR_rAAAAAJ","bQwCIGQAAAAJ","67LUQJUAAAAJ","Zxdn7DwAAAAJ"))

do.call(rbind, map(map(DF$GID, get_profile), 
                   function(x){data.frame(Person = x$name,
                                          Total.Cites = x$total_cites,
                                          h.index = x$h_index,
                                          i10.index = x$i10_index)}))

              Person Total.Cites h.index i10.index
1 Charles M. Cleland        6052      42       124
2  Samuel R Friedman       26259      85       349
3        Holly Hagan       40152      62       179
4     Danielle Ompad        5687      44        90

Generating Non-Random Data

seq(1, 10, 2)

[1] 1 3 5 7 9

104:114

 [1] 104 105 106 107 108 109 110 111 112 113 114

rep(c('A','B','C'), 3)

[1] "A" "B" "C" "A" "B" "C" "A" "B" "C"

rep(c('A','B','C'), each = 3)

[1] "A" "A" "A" "B" "B" "B" "C" "C" "C"

seq(1, 4, len = 6)

[1] 1.0 1.6 2.2 2.8 3.4 4.0

expand.grid(Person = 1:5, Visit = 1:3)

   Person Visit
1       1     1
2       2     1
3       3     1
4       4     1
5       5     1
6       1     2
7       2     2
8       3     2
9       4     2
10      5     2
11      1     3
12      2     3
13      3     3
14      4     3
15      5     3

Generating Random Data

rnorm(10)

 [1]  0.1608862  0.1912459  1.4058626  0.6708175 -1.0634520  0.4113199
 [7]  2.4238979 -0.2514567  0.3252108  0.7818911

runif(10, min=100,max=999)

 [1] 756.7219 363.0041 973.0582 810.7559 856.7343 522.0322 266.3716 772.0575
 [9] 133.1941 477.6735

rbinom(10, 1, .5)

 [1] 0 1 1 0 0 0 0 0 1 0

sample(letters[1:3], size = 30, replace=TRUE, prob = c(.8,.1,.1))

 [1] "a" "a" "b" "a" "a" "a" "a" "b" "c" "a" "a" "a" "a" "a" "a" "b" "b" "a" "a"
[20] "a" "a" "a" "c" "a" "a" "b" "a" "a" "c" "b"

sample(10)

 [1]  4  5  8  2  6  7  3 10  1  9

More on R Packages

• There is an App for that
• In R, there is a package for that
• ggplot2
  • plots
• dplyr
  • filtering
  • subsetting
  • variable creation
  • summarizing
• tidyr
  • reshape wide to long
  • reshape long to wide
• openxlsx
  • read and write MS-Excel files
• descr
  • frequency tables and crosstabs
• lme4
  • linear and generalized linear mixed effects
• data.table
  • efficient data table storage and powerful tools to manipulate data tables

Where and how to find R packages

• Comprehensive R Archive Network (CRAN; https://cran.r-project.org/mirrors.html)
• CRAN task views (https://cloud.r-project.org/web/views/)
• Google (e.g., “r-project psychometrics”)
• http://www.rdocumentation.org/
• R available.packages() function

How to install and load R packages

• Install
  • R install.packages() function
  • Part of the RStudio and RWindows menus
• Load a package to make content available to R
  • R library() function

install.packages("epiR")

library(epiR)
head(ls("package:epiR"), n = 30)

 [1] "epi.2by2"         "epi.about"        "epi.asc"          "epi.betabuster"  
 [5] "epi.bohning"      "epi.ccc"          "epi.ccsize"       "epi.cluster1size"
 [9] "epi.cluster2size" "epi.clustersize"  "epi.cohortsize"   "epi.conf"        
[13] "epi.convgrid"     "epi.cp"           "epi.cpresids"     "epi.descriptives"
[17] "epi.detectsize"   "epi.dgamma"       "epi.directadj"    "epi.dms"         
[21] "epi.dsl"          "epi.edr"          "epi.empbayes"     "epi.equivb"      
[25] "epi.equivc"       "epi.herdtest"     "epi.indirectadj"  "epi.insthaz"     
[29] "epi.interaction"  "epi.iv"          

Resources to Learn More

• http://www.r-project.org/
• http://www.rdocumentation.org/
• Springer Use R! Series (http://www.springer.com/series/6991)
• Cross Validated (http://stats.stackexchange.com/)